Rosetta
protocols::frag_picker::FragmentPicker Member List

This is the complete list of members for protocols::frag_picker::FragmentPicker, including all inherited members.

add_chunk_filter(VallChunkFilterOP filter)protocols::frag_picker::FragmentPickerinline
add_query_ss(std::string, std::string)protocols::frag_picker::FragmentPicker
add_scoring_method(scores::FragmentScoringMethodOP scoring_term, core::Real weight, core::Size index=1)protocols::frag_picker::FragmentPickerinline
atom_pair_constraint_contact_map_protocols::frag_picker::FragmentPickerprivate
bounded_protocol()protocols::frag_picker::FragmentPicker
candidates_sink_protocols::frag_picker::FragmentPickerprivate
candidates_sinks_protocols::frag_picker::FragmentPickerprivate
chunks_protocols::frag_picker::FragmentPickerprivate
contact_types_protocols::frag_picker::FragmentPickerprivate
contacts_dist_cutoff_squared_protocols::frag_picker::FragmentPickerprivate
contacts_dist_cutoffs_squared_protocols::frag_picker::FragmentPickerprivate
contacts_min_seq_sep_protocols::frag_picker::FragmentPickerprivate
count_query_ss()protocols::frag_picker::FragmentPickerinline
create_scores(std::string file_name)protocols::frag_picker::FragmentPickerinline
filters_protocols::frag_picker::FragmentPickerprivate
frag_sizes_protocols::frag_picker::FragmentPicker
fragment_contacts(core::Size const fragment_size, utility::vector1< Candidates > const &fragment_set)protocols::frag_picker::FragmentPicker
FragmentPicker()protocols::frag_picker::FragmentPickerinline
FragmentPicker(std::string fragment_score_manager_type)protocols::frag_picker::FragmentPickerinline
get_candidates_collector(core::Size frag_size, core::Size index=1)protocols::frag_picker::FragmentPickerinline
get_final_fragments(core::Size qPos, core::Size frag_size, Candidates &out)protocols::frag_picker::FragmentPicker
get_final_fragments(core::Size qPos, Candidates &out)protocols::frag_picker::FragmentPicker
get_frag_sizes() constprotocols::frag_picker::FragmentPicker
get_n_candidates() constprotocols::frag_picker::FragmentPicker
get_n_frags() constprotocols::frag_picker::FragmentPicker
get_picked_positions() constprotocols::frag_picker::FragmentPicker
get_query_phi_prediction()protocols::frag_picker::FragmentPickerinline
get_query_phi_prediction_conf()protocols::frag_picker::FragmentPickerinline
get_query_psi_prediction()protocols::frag_picker::FragmentPickerinline
get_query_psi_prediction_conf()protocols::frag_picker::FragmentPickerinline
get_query_residue_depth()protocols::frag_picker::FragmentPickerinline
get_query_sa_prediction()protocols::frag_picker::FragmentPickerinline
get_query_seq()protocols::frag_picker::FragmentPickerinline
get_query_seq_string()protocols::frag_picker::FragmentPickerinline
get_query_ss(std::string prediction_name)protocols::frag_picker::FragmentPickerinline
get_query_ss_string(std::string prediction_name)protocols::frag_picker::FragmentPickerinline
get_score_manager(core::Size index=1)protocols::frag_picker::FragmentPickerinline
get_self_ptr() constprotocols::frag_picker::FragmentPickerinline
get_self_ptr()protocols::frag_picker::FragmentPickerinline
get_self_weak_ptr() constprotocols::frag_picker::FragmentPickerinline
get_self_weak_ptr()protocols::frag_picker::FragmentPickerinline
get_vall()protocols::frag_picker::FragmentPickerinline
getFragSet(int residueInPose_)protocols::frag_picker::FragmentPicker
is_valid_chunk(VallChunkOP chunk)protocols::frag_picker::FragmentPicker
is_valid_chunk(core::Size const frag_len, VallChunkOP chunk)protocols::frag_picker::FragmentPicker
keep_all_protocol()protocols::frag_picker::FragmentPicker
log_200_protocols::frag_picker::FragmentPickerstatic
log_25_protocols::frag_picker::FragmentPickerstatic
max_frag_len()protocols::frag_picker::FragmentPickerinline
max_frag_size_protocols::frag_picker::FragmentPickerprivate
max_threads_protocols::frag_picker::FragmentPickerprivate
n_candidates_protocols::frag_picker::FragmentPicker
n_frags_protocols::frag_picker::FragmentPicker
nonlocal_min_contacts_per_res_protocols::frag_picker::FragmentPickerprivate
nonlocal_pairs(core::Size const fragment_size, utility::vector1< Candidates > const &fragment_set)protocols::frag_picker::FragmentPicker
nonlocal_pairs_at_position(core::Size const position, core::Size const &fragment_size, utility::vector1< bool > const &skip, utility::vector1< Candidates > const &fragment_set, utility::vector1< nonlocal::NonlocalPairOP > &pairs)protocols::frag_picker::FragmentPicker
output_fragments(core::Size const fragment_size, utility::vector1< Candidates > const &final_fragments)protocols::frag_picker::FragmentPicker
output_pair_counts(core::Size const fragment_size, core::Size const neighbors, std::map< std::pair< core::Real, ContactType >, ContactCountsOP > contact_counts)protocols::frag_picker::FragmentPickerprivate
parse_command_line()protocols::frag_picker::FragmentPicker
parse_quota_command_line()protocols::frag_picker::FragmentPicker
pick_candidates()protocols::frag_picker::FragmentPicker
pick_candidates(core::Size i_pos, core::Size frag_len)protocols::frag_picker::FragmentPicker
pick_chunk_candidates(VallChunkOP chunk, basic::thread_manager::RosettaThreadAssignmentInfo const &assignments)protocols::frag_picker::FragmentPicker
prefix_protocols::frag_picker::FragmentPicker
query_phi_prediction_protocols::frag_picker::FragmentPickerprivate
query_phi_prediction_conf_protocols::frag_picker::FragmentPickerprivate
query_positions_protocols::frag_picker::FragmentPickerprivate
query_profile_protocols::frag_picker::FragmentPickerprivate
query_psi_prediction_protocols::frag_picker::FragmentPickerprivate
query_psi_prediction_conf_protocols::frag_picker::FragmentPickerprivate
query_residue_depth_protocols::frag_picker::FragmentPickerprivate
query_sa_prediction_protocols::frag_picker::FragmentPickerprivate
query_seq_as_string_protocols::frag_picker::FragmentPickerprivate
query_ss_as_string_protocols::frag_picker::FragmentPickerprivate
query_ss_profile_protocols::frag_picker::FragmentPickerprivate
quota_protocol()protocols::frag_picker::FragmentPicker
read_depth(std::string const &file_name)protocols::frag_picker::FragmentPicker
read_psipred_ss2(std::string const &, std::string)protocols::frag_picker::FragmentPicker
read_spine_x(std::string const &file_name)protocols::frag_picker::FragmentPicker
read_ss_file(std::string const &, std::string const &)protocols::frag_picker::FragmentPicker
read_ss_files(utility::vector1< std::string > const &sec_str_input)protocols::frag_picker::FragmentPicker
read_talos_ss(std::string const &, std::string)protocols::frag_picker::FragmentPicker
read_vall(std::string const &fn)protocols::frag_picker::FragmentPicker
read_vall(utility::vector1< std::string > const &fns)protocols::frag_picker::FragmentPicker
save_candidates()protocols::frag_picker::FragmentPicker
save_fragments()protocols::frag_picker::FragmentPicker
scores_protocols::frag_picker::FragmentPickerprivate
selector_protocols::frag_picker::FragmentPicker
set_candidates_collector(core::Size frag_size, CandidatesCollectorOP sink, core::Size index=1)protocols::frag_picker::FragmentPickerinline
set_frag_sizes(utility::vector1< core::Size > size, bool clear)protocols::frag_picker::FragmentPicker
set_max_threads(core::Size const setting)protocols::frag_picker::FragmentPicker
set_n_candidates(core::Size n_candidates)protocols::frag_picker::FragmentPicker
set_n_frags(core::Size n_frags)protocols::frag_picker::FragmentPicker
set_picked_positions(core::Size, core::Size)protocols::frag_picker::FragmentPicker
set_picked_positions(utility::vector1< core::Size >)protocols::frag_picker::FragmentPicker
set_query_phi(utility::vector1< core::Real > &query_phi)protocols::frag_picker::FragmentPicker
set_query_phi_conf(utility::vector1< core::Real > &query_phi_conf)protocols::frag_picker::FragmentPicker
set_query_profile(core::sequence::SequenceProfileOP profile)protocols::frag_picker::FragmentPickerinline
set_query_psi(utility::vector1< core::Real > &query_psi)protocols::frag_picker::FragmentPicker
set_query_psi_conf(utility::vector1< core::Real > &query_psi_conf)protocols::frag_picker::FragmentPicker
set_query_sa(utility::vector1< core::Real > &query_sa)protocols::frag_picker::FragmentPicker
set_query_seq(core::sequence::SequenceProfileOP query_sequence)protocols::frag_picker::FragmentPicker
set_query_seq(std::string &query_sequence)protocols::frag_picker::FragmentPicker
set_selector(FragmentSelectingRuleOP selector)protocols::frag_picker::FragmentPickerinline
set_up_quota_nnmake_style()protocols::frag_picker::FragmentPicker
set_up_ss_abego_quota()protocols::frag_picker::FragmentPicker
set_vall(VallProviderOP vall_chunks)protocols::frag_picker::FragmentPickerinline
show_scoring_methods(std::ostream &out, core::Size index=1)protocols::frag_picker::FragmentPickerinline
sidechain_contact_dist_cutoff_protocols::frag_picker::FragmentPickerprivate
size_of_query()protocols::frag_picker::FragmentPickerinline
total_score(scores::FragmentScoreMapOP f, core::Size index=1)protocols::frag_picker::FragmentPicker
~FragmentPicker() overrideprotocols::frag_picker::FragmentPicker